Why use Affymetrix microarrays?

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Introduction to Affymetrix Microarrays
Why use microarrays? Permits expression profiling
of thousands of genes in parallel

• Why use Affymetrix microarrays?
• Well established platform
• Arrays for various species
• Enables combination of different applications
• Support from the bioinformatic community
• Well annoted probesets

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Introduction to microarraysSteps in analysis
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Introduction to microarraysAffymetrix
Instrumentation
Design Experiment
Prepare Sample
Wash Stain
Hybridize
Scan
Hybridization Oven
Scanner
Fluidics Station
Probe Array
Data Analysis Software
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Introduction to microarraysChip features
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Introduction to microarraysArrays and
Applications
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Introduction to microarraysAffymetrix
Applications
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Introduction to microarraysDevelopment of
Affymetrix technology
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Introduction to microarraysBioinformatic
flowchart
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Computer Lab -in silico microarray study
Title Molecular profiling of tumor progression
in NSCLC Geo id GSE7880 Array Affymetrix Human
HG-Focus Target Array Design
Primary Recurrent stage IIIB or IV
Adenocarcinoma (AC) 10 15
Squamous cell carcinoma (SCC) 10 8
http//www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc
GSE7880

• Lab tasks
• Download data set from GEO
• Add annotations from Affymetrix
• Perform t-tests to compare expression between
  groups
• Answer a set of questions using web resources

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Computer LabQuality Control of data